Rx side effects. These are not unusual side effects of proton pump inhibitors. How were you diagnosed with H. pylori? stool antigen or EGD in presence of an ulcer. The nexium is part of the therapy (approx. 14 days) for H. pylori. It would be reasonable to take yourself off of it for a few days or take a 1/2 dose. Contact your doctor re: time course necessary vs. optional. Longer tx typically used if ulcer.